I would say we should go radical in this question Relabs. Compatibility is a very important question.
Sure it went like this for years, but ultimately if you apply a modplug-only extension to any of the legacy format, it will become straight broken. Other trackers may or may not even load it. All the extended controls should be grayed out in them.
It could be an option to leave them available, but as soon someone would use them, a warning would appear, and the song could be only saved in MPTM format (while "exporting" could be still available, but then all the extended stuff should be ripped off from the song again in the process, to make the module perfectly compatible with outer programs).
It would be great to have some statistics how many people use VST's with XM's.
I would say about none, because vst and xm related stuff seems to be broken, as we figured out in this thread.

ideally MPTM would provide ability to choose between XM and IT commands.
Not sure about all the legacy tracker commands, but if there are differences between them (asides from notation), we should make two MPTM formats to avoid incompatibilities. MPTIT and MPTXM or anything simpler if you prefer.
If all the effects, their function and behavior are the same, but only the notation differs, it would be safe to have one MPTM forman, and only choose between effect notation on the song properties menu for instance.